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Querying over genomic ranges


Starting with InterMine 1.4 Bioseg is no longer required if you are using Postgres version 9.2 or later.

InterMine includes functionality for querying features with overlapping genome coordinates. We have an index that is created on the Location table. This is used by a ‘virtual’ SequenceFeature.overlappingFeatures collection that is a view in the postgres database using the index (either bioseg or the native Postgres one) to find other features that overlap it.

In modMine (the InterMine for the modENCODE project) we also create GeneFlankingRegion features to represent specific distances upstream and downstream of genes to query for genes that are nearby other features.

Install BIOSEG (Postgres versions 9.1 and older only)

BIOSEG is a custom index type that you need to add to postgres. See Range Queries for details

Create the index

You need to create the index on the location table in your production database by adding the create-location-range-index post-process step to your project.xml file:

<post-process name="create-location-range-index"/>

If you are using an older version of Postgres, this task will create a BIOSEG index. Otherwise it will use a native Postgres index.

Create the overlappingFeatures view

Create the SequenceFeature.overlappingFeatures view in the database. This allows you to query for any features that overlap any other types of features in the web interface or query API. Add the create-overlap-view post-process step, which needs to be located after create-location-range-index in your project XML file.

<post-process name="create-overlap-view" />

Now any queries on the overlappingFeatures collections will use this view and the new index.